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1a5u
From Proteopedia
(New page: 200px<br /><applet load="1a5u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1a5u, resolution 2.35Å" /> '''PYRUVATE KINASE COMP...) |
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| - | [[Image:1a5u.gif|left|200px]]<br /><applet load="1a5u" size=" | + | [[Image:1a5u.gif|left|200px]]<br /><applet load="1a5u" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1a5u, resolution 2.35Å" /> | caption="1a5u, resolution 2.35Å" /> | ||
'''PYRUVATE KINASE COMPLEX WITH BIS MG-ATP-NA-OXALATE'''<br /> | '''PYRUVATE KINASE COMPLEX WITH BIS MG-ATP-NA-OXALATE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Pyruvate kinase from rabbit muscle has been cocrystallized as a complex | + | Pyruvate kinase from rabbit muscle has been cocrystallized as a complex with MgIIATP, oxalate, Mg2+, and either K+ or Na+. Crystals with either Na+ or K+ belong to the space group P2(1)2(1)2(1), and the asymmetric units contain two tetramers. The structures were solved by molecular replacement and refined to 2.1 (K+) and 2.35 A (Na+) resolution. The structures of the Na+ and K+ complexes are virtually isomorphous. Each of the eight subunits within the asymmetric unit contains MgIIoxalate as a bidentate complex linked to the protein through coordination of Mg2+ to the carboxylates of Glu 271 and Asp 295. Six of the subunits also contain an alpha,beta,gamma-tridentate complex of MgIIATP, and the active-site cleft, located between domains A and B, is closed in these subunits. In the remaining two subunits MgIIATP is missing, and the active-site cleft is open. Closure of the active-site cleft in the fully liganded subunits includes a rotation of 41 degrees of the B domain relative to the A domain. alpha-Carbons of residues in the B domain undergo movements of up to 17.8 A (Lys 124) in the cleft closure. Lys 206, Arg 119, and Asp 177 from the B domain move several angstroms from their positions in the open conformation to contact the MgIIATP complex in the active site. The gamma-phosphate of ATP coordinates to both magnesium ions and to the monovalent cation, K+ or Na+. A Mg2+-coordinated oxygen from the MgIIoxalate complex lies 3.0 A from Pgamma of ATP, and this oxygen is positioned for an in-line attack on the phosphorus. The side chains of Lys 269 and Arg 119 are positioned to provide leaving-group activation in the forward and reverse directions. There is no obvious candidate for the acid/base catalyst near the 2-si face of the prospective enolate of the normal substrate. A functional group linked through solvent and side-chain hydroxyls may function in a proton relay. |
==About this Structure== | ==About this Structure== | ||
| - | 1A5U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with NA, OXL, MG and ATP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pyruvate_kinase Pyruvate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] Full crystallographic information is available from [http:// | + | 1A5U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=OXL:'>OXL</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ATP:'>ATP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pyruvate_kinase Pyruvate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A5U OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Pyruvate kinase]] | [[Category: Pyruvate kinase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Benning, M | + | [[Category: Benning, M M.]] |
| - | [[Category: Larsen, T | + | [[Category: Larsen, T M.]] |
[[Category: Rayment, I.]] | [[Category: Rayment, I.]] | ||
| - | [[Category: Reed, G | + | [[Category: Reed, G H.]] |
[[Category: ATP]] | [[Category: ATP]] | ||
[[Category: MG]] | [[Category: MG]] | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:41:11 2008'' |
Revision as of 09:41, 21 February 2008
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PYRUVATE KINASE COMPLEX WITH BIS MG-ATP-NA-OXALATE
Overview
Pyruvate kinase from rabbit muscle has been cocrystallized as a complex with MgIIATP, oxalate, Mg2+, and either K+ or Na+. Crystals with either Na+ or K+ belong to the space group P2(1)2(1)2(1), and the asymmetric units contain two tetramers. The structures were solved by molecular replacement and refined to 2.1 (K+) and 2.35 A (Na+) resolution. The structures of the Na+ and K+ complexes are virtually isomorphous. Each of the eight subunits within the asymmetric unit contains MgIIoxalate as a bidentate complex linked to the protein through coordination of Mg2+ to the carboxylates of Glu 271 and Asp 295. Six of the subunits also contain an alpha,beta,gamma-tridentate complex of MgIIATP, and the active-site cleft, located between domains A and B, is closed in these subunits. In the remaining two subunits MgIIATP is missing, and the active-site cleft is open. Closure of the active-site cleft in the fully liganded subunits includes a rotation of 41 degrees of the B domain relative to the A domain. alpha-Carbons of residues in the B domain undergo movements of up to 17.8 A (Lys 124) in the cleft closure. Lys 206, Arg 119, and Asp 177 from the B domain move several angstroms from their positions in the open conformation to contact the MgIIATP complex in the active site. The gamma-phosphate of ATP coordinates to both magnesium ions and to the monovalent cation, K+ or Na+. A Mg2+-coordinated oxygen from the MgIIoxalate complex lies 3.0 A from Pgamma of ATP, and this oxygen is positioned for an in-line attack on the phosphorus. The side chains of Lys 269 and Arg 119 are positioned to provide leaving-group activation in the forward and reverse directions. There is no obvious candidate for the acid/base catalyst near the 2-si face of the prospective enolate of the normal substrate. A functional group linked through solvent and side-chain hydroxyls may function in a proton relay.
About this Structure
1A5U is a Single protein structure of sequence from Oryctolagus cuniculus with , , and as ligands. Active as Pyruvate kinase, with EC number 2.7.1.40 Full crystallographic information is available from OCA.
Reference
Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel., Larsen TM, Benning MM, Rayment I, Reed GH, Biochemistry. 1998 May 5;37(18):6247-55. PMID:9572839
Page seeded by OCA on Thu Feb 21 11:41:11 2008
Categories: Oryctolagus cuniculus | Pyruvate kinase | Single protein | Benning, M M. | Larsen, T M. | Rayment, I. | Reed, G H. | ATP | MG | NA | OXL | Transferase
